On Mon, Nov 7, 2011 at 2:26 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > >> Dear Gmx Users, >> I know that this problem has been discussed may times but I cannot find >> the solution to get rid of pbc in my system: protein and ligand. I followed >> the workflow: >> >> 1. First make your molecules whole if you want them whole >> >> trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc >> >> 2. Cluster your molecules/particles if you want them clustered >> >> 3. Extract the first frame from the trajectory as reference for >> removing jumps if you want to remove jumps. >> >> trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb >> >> 4. Remove jumps if you want to have them removed using the first >> frame >> >> trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc >> >> 5. Center your system using some criterion. Doing so shifts the >> system, so don't use |trjconv -|pbc| nojump| after this step. >> >> >> trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc >> >> 6. Put everything in some box. >> >> trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o >> mdwholeNOjumpCENTERbox.xtc >> >> 7. Fit if desired and don't use any PBC related option afterwards. >> >> trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o >> mdfinal.xtc >> >> >> I used SYSTEM everywhere as output orinput. However, my ligand is still >> jumping like a fly around the stable protein. Do you have any suggestions? >> >> >> > > Center on either the protein, the ligand, or some custom index group of > residues surrounding the ligand. Centering on the whole system usually > doesn't do anything useful. > > -Justin > > Thank you guys but... I am trying and it does not work... my ligand is jumping like an idiot outside the box changing its position even two dimensions of box in one frame. I removed -ur compact from the first line and I tried centering on ligand or protein (centering group: LIG or Protein, output: SYSTEM). No results... My ligand at the begining of the simualtion is not within the protein. Please, help :(((( I tried this workflow with many ligands and same protein - it worked! Now it does not... Here is my workflow: 1. First make your molecules whole if you want them whole. trjconv -f md.trr -s md.tpr -pbc whole -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame (system) trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step (tried centering on LIG or PROTEIN) trjconv -f mdwholeNOjump.xtc -n Ligand.ndx -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc With point three, the issue is that trjconv<http://www.gromacs.org/Documentation/Gromacs_Utilities/trjconv>removes the jumps from the first frame using the reference structure provided with -s. If the reference structure (run input file) is not clustered/whole, trjconv -pbc nojump will undo steps 1 and Steven ==============================**========== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
